on it. Even if jessie repos are disabled, it is much easier to keep it clean. The fact that you left them makes us doubt you did do it right. The upgrade, that is. If you don't use source packages, you can delete them too (the ones that start with deb-src).

It's there until I get everything going, hence the commented out Jessie lines.

It'll get cleaned up once I've sorted out this issue.

And I did follow each and every step from the procedure, including returning my system to a pure Jessie install, which meant removing all backports and proprietary NVidia drivers and updating before doing the Jessie-Stretch upgrade.

To make a pure Jessie system prior to the upgrade (as per the upgrade instructions), I switched to the 3.18 kernel and purged all of my custom kernels. I did not check whether the patch was applied to the 3.18 kernel in Jessie. I assume it would have been after this length of time.

Now to install the 4.9 kernel from Stretch and fsck the filesystems before going further,

so the cloudfront server (and the error associated with this) disappeared from 'apt-get update's output after you delete a file in /etc/apt/sources.list.d?i honestly don't think this is data coruption, but something very fishy going on on your system.for your own sake, check it out.some softwares provide debian packages, and install their own sources.lists along the way. not good practice imo.